The health secretary will "franchise" the running of the NHS to a quango for up to three years at a time – a move that will result in an unelected academic and the nation's 38,000 family doctors, rather than ministers, being accountable for the day-to-day running of the health service, according to leaked documents obtained by the Guardian.

In unpublished evidence to the health select committee last week, Malcolm Grant, the government's choice to run the powerful NHS commissioning board, outlined "an extraordinary transformation of responsibility" that appears to undermine claims by ministers that the proposed legislation will not dilute the government's constitutional responsibilities to the health service.

At present, the cabinet minister for health has a "duty to provide a national health service" in England, but that disappears in the NHS bill's proposals.

Grant, a law professor who runs University College London, told MPs that, under the new system, the secretary of state "mandates" the commissioning board to run the NHS every "two … possibly three years" and then retreats into the shadows. The board will hand over taxpayers' cash to groups of GPs to buy services on behalf of patients.

He admitted there would be "a fundamental change of responsibility and accountability under the bill" because about £80bn of public money would be transferred to the board and GPs. He said these two groups – not politicians – would run the NHS and ensure patients received an adequate level of health provision in England.

"If [GPs] are dissatisfied with what happens in a hospital, they need to deal with it and not simply complain to a secretary of state who no longer has this responsibility, nor to the commissioning board which has given them the responsibility, but to complain to the hospital and get it sorted, and, if it is not sorted, to use their commissioning power to ensure that it is."

With peers beginning line-by-line scrutiny of the coalition's NHS bill on Tuesday, the government has been attempting to rebut detractors of all political persuasions influenced by the powerful Lords constitutional committee.

The committee warned last month about the "extent to which the chain of constitutional responsibility as regard to the NHS [will be] severed". In what is perceived as a sign of panic over the level of peers' opposition, a 72-page letter from ministers sent to all peers last week conceded a "necessary amendment" might be needed to rectify the impression the government would not be "responsible and accountable" for the NHS.

However, Grant, who is expected to take up the post later this month, confirmed the bill's critics' worst fears in a combative parliamentary performance last week.

In a remarkable admission, Grant told MPs that, from April 2013, in the event of a "crisis" in the health service. either he, nurses, GPs or hospital medical directors would be taking to the airwaves as the health secretary would not have responsibility for the daily running of the NHS.

"It is no longer going to be the case that the secretary of state is wheeled in front of the TV cameras," he told MPs. "Responsibility has to go back to where it is. It has to go back to within those hospitals. Who is the chief nurse? Who is the medical director. Where is the CEO?"

MPs questioned how the public would be informed how well the NHS was faring by asking who "will be the person doing Panorama?" Grant replied: "I said this job was full of risks and probably that ends up being one of them."

Parliamentary scrutiny will also become a thing of the past. After the bill is passed, the health secretary will no longer have to answer MPs' questions every month but will just put forward an annual report on how the board is doing once a year.

The secretary of state will also, in effect, lose "powers of direction" over the health service, depriving the minister of the power to order NHS services to improve. The government would find it difficult to repeat Labour's 2007 act of ordering a "deep clean" of NHS hospitals to tackle a rising tide of MRSA infections.

Lady Thornton, Labour's shadow health minister in the Lords, said: "This completely undermines the 1948 and 2006 acts. The whole point of the debate we've been having is that the secretary of state has to be accountable to parliament for the provision of a national health service, and you can't just start franchising out that role."

To smoke out the government, Labour has also put down a probing amendment before peers which asks the house to concede that the principles of the NHS should be to "promote quality, equity, integration and accountability, not the market".

A Department of Health spokesman said: "The secretary of state will remain responsible for promoting a comprehensive health service and retains the ultimate accountability for securing the provision of services, through his relationship with NHS bodies."